Sounds like your sqlite database got corrupted or something. Sqlite databases are just a file on disk. You could download the latest version of mojoPortal for Sqlite and just replace all the files with the new version, that would overwrite the database file with a new one.
Myself I would not use Sqlite, our SqlCE package is similar in that it is a file based database but it is a little more robust than Sqlite. But if you change to SQL Ce, I would just install it again in a new location or delete all the existing files if you want to install it in the same location.
The main benefits of Sqlite and SqlCE is that it does not require any database server software installed so deployment and installation are easier, but these databases are only good for low to medium traffic sites. If you plan a site to get a lot of traffic it is better to use a server based database like MS SQL or MySql.
Hope that helps,
Joe